Thanks everyone
@Neirao
Thanks for that script, but that was for snapping points together, not straightening out the lines.
Basically as I said, we just need a script that acts like the original Flatten command in anim8or, but works with lines and points also. I can't tell you after hours and hours of point modeling, some of the lines are at a slight angle. Which on some models can ruin the look, if we had script that could make sure the lines are straight it would make modeling a lot easier.
This is script that I think everyone would use, maybe Steve could implement a version of it with command prompt like the original flatten command, or even work it into the original some how?